Alpha and Omega: the Cruel Angel's Thesis
by soul-of-tabris
Summary: The only way to save humanity is to stop the Human Instrumentality Project. See the Warnings and Disclaimers for more details.
1. Warnings and Disclaimers

**Warnings and Disclaimers**

Neon Genesis Evangelion does not belong to me. OK? I admit it. GAINAX owns it, as well as many other entities who make a boatload of money off a more-than-worthy franchise. Me? I'm just another rabid Eva fan, so don't mind me!

Secondly, this story has many pairings in it. Some are het and one major one is shounen-ai. I'll let you guess as to which pairing that is. All pairings are kept to light kissing and hugging and there is no sex (or anything close to it), hence the PG-13 rating. Does that intrigue you? Then read on! If not, depart now with no hard feelings on my part or yours.

Thirdly, as much as I adore Kaworu, I have to admit that I was tired of reading about Mr. I'm-So-Sweet-I-Can-Make-You-Gag Kaworu. I wanted a harder-edged Kaworu. That is the type of Angel Boy you'll find in this fic. Those looking for a gentler Kaworu will probably want to leave now, as my version of Kaworu is kind of intense!

Lastly, this fic is an A/U that asks a question: what if the only way to save humanity was to stop the Human Instrumentality Project before it kicked into gear? Though many aspects of the Eva story are the same, Shinji and Asuka grew up as childhood friends in this story and did not receive any Evangelion training. Asuka is still ridiculously bright and attractive and popular; Shinji is still introverted and sort of wimpy (heh heh). Other Eva characters make appearances. You'll see what I mean!

Well, that's it. If you read all of this, I thank you. I hope you enjoy my bastardization of Evangelion!


	2. Chapter 1: Twin Souls Adrift

_Italics _indicate thoughts.

----

            Blue.  Like the summer sky over Tokyo-3.  

            A breeze tussled Rei's chin-length bob.  She smoothed it quickly with her open palm, but the wind toyed with her ends again.  It was determined to have its way.  Her fight was in vain.

            To another, her concern about her hair was a small thing.  To Rei, it marked her.  She was not blind.  No one else had hair the color of a cloudless summer sky.  Blue.  Like a freak.  The unspoken hung like a mist around her, clung to her clothes and her hair and eyes.  No one had to say it.  Rei already knew it.  She was set apart from everyone else, on a fundamental level that no one cared to elaborate.

            Even on the days when she was allowed to leave the bowels of NERV, she sensed their amusement.  They were in on the joke.  She could only go through the motions, pretending to be normal when everyone knew that Rei was different.  They humored her.  She had no choice but to wallow in the deception.

            She hated them.  Her hate was fed by her inherent need, though.  She needed them.  She knew of no other life but endless prodding by doctors and daily training to pilot a monstrosity that was somehow related to her.

            _Do you know what an Evangelion is?_

And how was she related to it?  And why did they whisper over and around her about the Evangelions and the strange girl with the bobbed blue hair?

            She hated NERV.  Even as their guards watched her sitting on the park bench … she hated them as well.  All of them, she hated them all.

            Folding her hands on her lap, she sighed.  There were no pigeons to feed this day.  The small bag of feed in her lap was for naught.  She did not know if she was sadder for the birds or for herself.

            Someone stepped directly in front of her, blocking the sun from her face.  The light spilled around the tall and lean figure, darkening his body until it was a silhouette against the noon sun.

            "May I sit down?"

            He took a step back, and his features came into focus.  The sunlight played in the boy's hair, sparkling and glistening against its unruly silver and gray strands.  He had very pale skin.  Rei could not help but wonder why his skin looked like hers.

            "I see you have red eyes as well."

            She blinked, and looked again.  His eyes were open, and indeed, they were bright and shining and crimson.  Like her own eyes.  Like her …

            The boy grinned.  Rei wondered if she was showing her surprise.  Perhaps her slacked jaw was a clue.  Still, she pushed past her curiosity and shock long enough to ask, "Will you sit down?"

            "I'd be delighted."

--------

            They sat in silence for a time.  She kept her hands folded in her lap and tried to process her thoughts carefully, though it was difficult.  Just the sight of the boy, who looked just like her, answered a few questions she had pondered in the past.  Still, there was more to learn.  What did he know?  

            "You never asked my name."  It was an astute observation on her part and was stated as such.

            The boy turned to Rei and smiled before answering.  "I imagine that you go by many names, like me."  His eyes fell on her, and she met his look directly.  He made her nervous, though she did not know why.  "What name should I use?"

            "I am Rei Ayanami."

            He nodded.  "It is an honor to meet you, Ayanami-san.  I am Kaworu.  Kaworu Nagisa."

            "I see."  An unfamiliar name to match a familiar face … the mystery deepened in Rei's mind.  "Nice to meet you, Nagisa-san."

            "Call me Kaworu, Ayanami-san."

            As if he had known her forever, he wanted her to call him by his first name.  Rei could not help but marvel at the odd boy.  His bizarre features were the biggest clue that they were related; some part of her was appalled that she could be associated with someone who was so peculiar.  Still, Kaworu intrigued Rei.  

            "I am here to do more than exchange names, Ayanami-san."

            He was unlike anyone she had ever met before.  Rei did not know if that was good or bad just yet.

            "Do you know why we look alike?"  Kaworu cut to the biggest question right away.

            She could only shake her head.

            "We both have a purpose … we were created with a destiny.  We are supposed to aid in the Third Impact."

            _Third Impact?  Created?  Destiny?_  The weight of oncoming answers weighed on Rei's mind heavily; Kaworu definitely knew something.  Just from those words alone …

            "I'm not interested in following their script … you weren't informed, were you?"

            Again, she shook her head.  

            "Figures.  I have quite a tale to tell, Ayanami-san.  But first, I have to get you out of here.  Do you fly?"

            Rei could no longer suppress her surprise.  "Fly?" was her bewildered response.

            Kaworu looked away for a moment.  He seemed a bit disappointed.  "I'll take that as a 'no'.  Nothing can ever be too easy, now can it?  Well, there are ways around that."  The grin that spread across the boy's face seemed wide enough to split his face in half.  He hardly looked human.  Rei wondered if that was the point.

            "Tell me, Ayanami-san, about your two guards … are they nice to you?"

            Rei did not ask how Kaworu knew about her guards or even knew the precise number of men who watched her when she left NERV.  "Hmm?"

            "They have never hurt you, have they?"

            "No," she answered.

            "Good.  I won't kill them, then."

            The atmosphere changed just as Kaworu stopped speaking.  Something fundamental shifted; the air became thick and heavy.  Even as others in the park continued about their business – walking and talking amongst themselves – Rei felt a new frequency assault her senses.  Hairs she did not even know she had were standing on end.  

            A yell broke the reverie.

            Rei turned in time to see the uniformed guard fall to his knees.  His eyes, full of fear, seemed to look past everything.  The man's fingers dug into the sides of his face, threatening to break the skin.  He let out a silent scream before he passed out.

            Another man, dressed in a jogging suit, was propped up against a tree only a few feet away.  Horror had etched itself on his face.  Intermittent twitching was the only evidence that the plainclothes guard was still alive.

            When Rei turned to set her eyes on Kaworu, she saw that his face was impassive, almost as if he was ethereal.  Not of the earth.  But there was something more in his wide eyes.  A raw thing laid behind those eyes … a power unconcerned with civility and morality, something older than the laws of man.  Kaworu was looking in their direction, and to an untrained eye, it would seem that he was looking at the men.  Rei knew better.  Even as passerbys noticed the men and rushed to their aid, she remained still and kept her eyes on Kaworu.

            _Am I like that?_  The random thought smacked Rei across her face.  _Is this why they fear me?_

"They are in no danger of dying, Ayanami-san."  Kaworu was calm, almost dismissive.  Like a simple mathematical equation, the solution was quick and decisive.  The ends justified the means.  "My influence is temporary, after all."  He blinked, and turned to look at Rei.  The primal stare had melted away; all that remained were the kind eyes of a child.  "You have a choice, Ayanami-san.  Would you like to take a walk with me?"

            He held out his hand.  It was unsteady and shivering.  Like a child.  Rei had to remember that he was a child, just as she was.  Maybe they were alike.  Maybe that was all she needed to leave her past behind.

            Rei did not fully understand why she placed her hand in Kaworu's open palm.  When Kaworu pulled Rei closer to him and their fingers intertwined, her rising blush provided at least some answer behind her motivation.  She tried not to think on that, though.  It seemed the silliest reason of all to leave:  that she would toss everything away to pursue a crush.

            The two walked away from the crowd gathering around the unconscious guards.  Rei did not look back.                        


	3. Chapter 2: Their Eyes Were Watching God

            No one wanted to believe that Rei Ayanami was gone, least of all Gendo Ikari.  It was like losing Yui all over again; the only way the man could bear it was to bury himself in the business of retrieving Rei.  It was not easy.  Rei was nowhere to be found.  After several weeks of searching, no one at NERV knew where to begin.

            That is, until the explosions began.

            Evangelion facilities in America and China and Germany had been destroyed.  The attacks always happened in the early morning.  No one had been killed, though some workers told of being incapacitated and finding themselves outside of the harm's way watching their place of employment come to ruin.  

            "Only Eva factories are being targeted."

            "Very few groups know what's being made.  Very few people know what an Evangelion is."  Fuyutsuki placed a folder of collected information on Gendo Ikari's desk.

            Only one group remained in possession of Evangelions.  Gendo Ikari knew that it was only a matter of time.  He also did not dismiss the possibility that the attacks and Ayanami's disappearance were related, as the two happened within a short time frame.

            "Do you think SEELE is behind this?"

            Gendo Ikari would have liked nothing more than to take the old men head-on, but the attacks were not their style.  SEELE had panache.  The attacker in question was not at all like the old men.  "There's no need for them to be so heavy-handed when there are no Angels.  Besides, those factories were built with SEELE money.  The old men would rather fall on their swords than waste money."

            Fuyutsuki shivered visibly despite himself.  Gendo Ikari's classic stony nature had become even more hardened since Ayanami was lost.  It unnerved Fuyutsuki that such a man as Ikari could be even more ruthless than usual.  "So we're dealing with someone else?"

            A picture slipped halfway out of the folder.  It was evidence taken from the destruction in America, at a facility in Utah.  The facility had burned to the ground.  All Evangelions – prototype and completed – as well as data were lost.

            Eyewitnesses said that when the explosion occurred, a pillar of flame in the shape of a cross shot into the air, a rather memorable sight against the darkened sky.

            "Are we so sure this isn't the work of an Angel?"

            "The Dead Sea Scrolls don't …"

            "Forget about the Dead Sea Scrolls.  We could be dealing with whoever took Rei.  Don't forget about that.  We need her."

            Fuyutsuki bit back the obvious:  that Gendo Ikari needed Rei Ayanami, that she had worth beyond her duties in the Human Instrumentality Project.  Instead, the former professor only nodded.  Gendo Ikari turned in his chair, and that was Fuyutsuki's cue to leave the room.  He did so without another word.

            Gendo Ikari sighed.  He was closer than ever to finding Ayanami and retrieving that necessary piece of the puzzle in the larger project.  All he needed was for the attacker to reveal himself.  NERV held the last Evangelions on earth.  Soon, the attacker would be dealt with and he could return to much more important business.  

            A small kink in the plans … that was all it was.  Gendo Ikari assured himself that there would be no more distractions.  He would achieve his intended goal.

            "Yui …"

--------

            In a darkened room, far from prying eyes, the men of SEELE gathered to assess the damage.

            "Five facilities in three months … this is not good news."

            "What do we pay those security officers for if they can't stop destruction like this?"

            "This is a flagrant waste of money!  Who knows how far the project has been set back?"

            "Perhaps NERV is involved."

            Keel Lorenz leaned forward, pondering the situation.  SEELE had created NERV.  SEELE had also created Kaworu.  Both entities threatened to destroy SEELE, and Keel Lorenz wanted nothing more than to wipe both wayward creations from the face of the earth.  However, one thing at a time … he could not afford to make a scene.  And though Gendo Ikari was no doubt an untrustworthy and dangerous opponent, Kaworu was even more dangerous.  That was a fact.

            "NERV is sniffing around, but I doubt they are involved.  Besides, there is a rumor that they have lost something equally precious to them."

            "There is another one?"

            "It is unconfirmed, but likely."

            "Gendo Ikari … that wily bastard!"

            "There is time enough to deal with Ikari.  Kaworu is a loose cannon.  The project cannot continue until this flawed incarnation is scrapped and we can begin anew."

            "Is that an authorization?"

            Keel Lorenz nodded.  "Yes.  Kill him on sight."

            The other men nodded as well.  The only way to bring the Human Instrumentality Project back to order was to regain control of an important key in the process.  Kaworu Nagisa had to be destroyed.        


	4. Chapter 3: A Brand New Day

_Italics _indicate thoughts.

/ Speech /  indicates instant messages.

Still with me?  Great!

----      

Shinji was aware of girls.  He was aware of his best friend, Asuka.  Beautiful Asuka, popular Asuka, never-have-a-chance-with-perfection-like-that Asuka … as it was, Shinji was grateful enough just being her friend.  That he was the frequent focus of her verbal barbs was of little consequence.  It was Asuka abusing him; in the end, Asuka-abuse was the best abuse a fourteen-year-old boy with little more than hormones and hope could ask for.

            As was usual for the morning walk to school, Asuka broke the peaceful stillness in Shinji's mind.  "Shinji-baka!  You weren't listening!"

            "Yes I was!"  Shinji knew it to be a lie even before he said it.  Every morning was the same:  Asuka talked as Shinji watched her mouth and waited for the words that would not come.  _Shinji, my parents left for the weekend and I was wondering … wanna come over?  I've liked you this whole time.  You're so cool, Shinji!  _

            Shinji knew better, even as he dared to dream.

            Asuka – not the compliant girl in his dreams, but the waking and walking nightmare – narrowed her eyes.  "Dumpkoff!  You think I'm stupid?  You didn't hear a word I said!"

            "Like it was important," Shinji mumbled.

            "Everything I say is important, baka!"

            Shinji just rolled his eyes.  It was the same conversation every morning.

            Asuka tossed her brilliant copper mane.  Her face had changed; the random fury was gone and in its place was an attempt at sensuality.  Shinji hated himself, that such a childish display of her power over him was so effective.  "Anyway, Shinji-baka, I need you to do something for me."  She turned to face him.    

            He could not blame Asuka.  It was his fault.  She did not even have to ask nicely for his help.  His affirmative was implicit, always there for her to exploit.  No one understood this more than Asuka.  Shinji despised his weakness.

            "What is it?"

            "I need you to show some new students around the school today."

            "Isn't that the job of the sophomore class president?"  Masochism prevailed over Shinji's common sense.  He did not know why he even bothered to feign resistance.  In the end, Asuka always got what she wanted. 

            "I've got a date that I've got to get ready for after school!"

            "A date?"  The knife plunged into his chest, threatening to go deeper.  Still, Shinji had to know.  "With who?"

            "Ka … ji … SAN!"  Asuka hugged herself and gleefully skipped.

            Shinji wanted to crawl into the nearest hole and promptly die.  Pondering the mystery behind his need to punish himself by being near Asuka, Shinji hung his head.  His eyes shifted away.

            "So, baka!  The new kids will meet up with you in homeroom.  Don't forget to introduce them to the fabulous and beautiful sophomore class president!"  

            Shinji looked up in time to see Asuka wink at him and walk towards the school.  The school … only a few yards away, Shinji only just noticed that they had already arrived.  

            Every morning was the same.  He walked to school with the girl of his dreams.  The girl of his dreams would tease and taunt and generally make Shinji feel like the biggest idiot walking the face of the earth.  Then, she would wink and wave and walk away.  Shinji could not help but wonder if all girls were like Asuka.  Why did he endure the endless abuse?

            A breeze caught the hem of Asuka's skirt and lifted it; a brief glimpse of Asuka's shapely, cream-colored thighs immediately became visible.  Like a sign of God's benevolence, Shinji saw it and understood.  Everything was worth it.

            Shinji gathered himself, and walked the rest of the way to the school doors.

--------

            "Class, we have two new students."  Ritsuko Akagi-sensei turned her back to her class.  As she wrote two names on the chalkboard, the two students standing in front of her desk bowed deeply before the seated class.

            The boy was tall and thin and eerily pale.  His hair was silver and gray, definitely an unusual color for a boy his age.  The white shirt was immaculately pressed, yet it fit awkwardly on the boy's lean frame.  His dark pants were also ironed and creased, but still appeared peculiar.  It was as if the boy did not belong in a school uniform … as if he was never meant to wear a school uniform.  

            Shinji could not place why he was noticing the boy, and what that meant. 

            "I am Kaworu, Kaworu Nagisa.  Pleased to meet you."

             _Stop looking_, Shinji admonished himself.  

            Kaworu displayed a grin so wide it seemed unnatural, but was still disarming.  Charming, even.  As Kaworu opened his eyes and the aggressively cheerful grin faded slightly, Shinji noticed Kaworu's eyes.  Red.  The color of blood.

            Those blood-colored eyes immediately found Shinji.  Kaworu's gaze was unreadable, but it grabbed Shinji's attention and did not let go.  Shinji felt his breath catch in his throat.  Like he had seen the strange boy before, he felt an odd familiarity with him.  Deja vu.

            Shinji shook his head.  That had to be wrong.  He would remember someone with such strange features.  He had never seen Kaworu before in his life; that much he knew to be true.

            The grin on Kaworu's face twisted itself into a smirk.

            A girl stood beside Kaworu.  Only shorter by an inch or two, she had bobbed blue hair and waxen skin and red eyes … just like Kaworu.  Her eyes were also red.  Shinji wondered if the two were related.

            "I am Rei Ayanami.  Pleased to meet you."  Her inflection was flat and bland, unlike Kaworu's gregarious greeting only moments before.  Shinji's certainty of the two's relation faltered, as their personalities seemed like night and day.

            Kaworu and Rei seated themselves at two desks in the far corner of the classroom.  Shinji looked back for a moment at the two.  He could hear Asuka – only a couple of desks away to his right – mumbling to Hikari about "the new weirdos".  Opening his laptop, Shinji just shrugged and prepared to focus on the class work at hand.

--------

            A blinking envelope in the right-hand corner of Shinji's laptop screen provided a much-needed distraction from studying.  It was probably Kensuke wanting to borrow notes or Touji making a comment about a random girl wearing a short skirt.  Shinji directed his cursor to the fervently blinking envelope and clicked.

            / You are Shinji Ikari-kun, right? /

            Shinji blinked.  That was odd.  No one messaged him but Kensuke or Touji … he could only dream of the day when Asuka would instant-message him, though that day had not come.  Suspecting a joke on the horizon, Shinji responded all the same.

            / Yes. /

            / That is good.  Will you be showing Rei and I around school today? /

            Shinji's eyes widened before he even realized it.  This was one of the new kids messaging him.

            / Who are you? /

            / Kaworu Nagisa.  Pleased to meet you. /

            / Nice to meet you, Nagisa-san. /

            / Call me Kaworu, Ikari-kun. /

            A brief glance over his shoulder, and Shinji confirmed that Kaworu was typing on his laptop.  Kaworu's eyes lifted, and met Shinji's curious look with a half-lidded gaze.  Shinji felt his cheeks beginning to burn, so he hastily turned around in his seat and returned to his laptop.

            / You can call me Shinji, Kaworu-kun. /

            / I am glad, Shinji-kun. /

            Kaworu addressed Shinji as if they had known each other all their lives.  It was embarrassing and endearing all at once.  Shinji lowered his head so that the laptop hid his reddening face.

            / Shinji-kun, will you be showing Rei and I around school today? /

            / Yeah … it's really not my job, but I'm doing it for a friend. /  

            Shinji pressed the "enter" key, but immediately regretted it.  His words carried an unintentional air of reluctance.  Maybe Shinji had grudgingly accepted his duty, but he had to admit that being around Kaworu made the chore seem, well, less like a chore.  The other boy was bright and friendly; doubt crept into the corners of Shinji's mind.  He just knew that he had offended Kaworu.  Before he even had a chance to know the other boy, Shinji had ruined everything.  He imagined that Kaworu hated him by now, and that the next instant message would be a cold and cruel rebuff to match Shinji's careless words.

            The envelope blinked again.  With a heavy heart, Shinji clicked on the envelope and awaited a prickly response.

            / What a kind friend you are, Shinji-kun.  How thoughtful of you to help your friend!  I am glad that you are the one showing Rei and I around our new school. /

            / We should meet after class and I'll show you around then, OK? /

            / I look forward to it, Shinji-kun. /

            Shinji did his best to cover his embarrassment from the rest of the class by hiding his face in his hands.  Kaworu saw this and smiled.  Rei looked at Kaworu, then Shinji, and returned her attention to an open textbook.


End file.
